The Dark Side of McKay
by Phoenix Nova
Summary: What if the ascension machine had an adverse effect on your conscience? What if McKay wanted to take over the city for his own evil purposes? Tao of Rodney spoiler-ish
1. Ch 1 The Accident

I don't own Stargate Atlantis, or any of the characters or actors, if I did own SGA, it would be in season 6 right now, looking forward to season 7.

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**Stargate Atlantis: The Dark Side of McKay**

**Chapter 1: The accident.**

A team of scientists, led by Dr. Rodney McKay and Dr. Radek Zelenka, explore a darkened corridor of the huge city. Water logged furniture and debris are scattered haphazardly in the corridor.

"She used to leave the lights on, all over the house. Every room. Drove my father nuts." McKay whined, referring to his sister, Jeanie.

Radek just chuckled. "For me, it was my brother. Only we had no lights. He used to leave candles burning everywhere." Zelenka reminisced.

"Well, you know what? No one wants to hear any more stories about how poor you were as a child, all right? We already feel as sorry for you as is humanly possible." McKay complained, hoping to end the story.

Radek directed his next comment to Dr. Esposito

"Uh, he burned the house down, you know?" Radek said, concluding his tale.

"My sister was afraid of the dark, and used to blame me for leaving the lights on. Of course, my father believed her. He never sided with me." Rodney complained, redirecting the attention to himself.

"We had to live in a tent in the dead of winter for three months." Radek added, ignoring Rodney's comment. This annoyed Rodney.

"You know, at least my stories relate to what we're doing." Rodney complained.

"Well, so do mine!" Zelenka defended.

"We're trekking all over the city, shutting down everything the Ancients activated while they were oh so briefly in control, so we can stop the power from draining from our one precious ZPM. How does that relate to your idiot brother burning the house down?" Rodney challenged.

"Okay, if we don't succeed" Zelenka began, but Rodney thoughtlessly interrupted.

"We're not going to have to live in a tent in the dead of winter!"

"It's a metaphor." Zelenka clarified.

Doctor Esposito ran her scanner over one of the closed doors, then called for McKay, Zelenka was behind Rodney.

"The control panel, it's completely shot." Esposito determined.

McKay brushes close to her as he forces himself past to the control panel. And once more demonstrates his PHD in sarcasm, and what a gentleman he's not.

"Really? You think so? You know, I don't get these Ancients. They're supposed to be so smart? Then why activate something that you don't need and you're not using, huh?" Rodney griped.

Zelenka shrugged.

"Well, maybe they didn't have time to get to it, you know, before the human form Replicators that you reprogrammed attacked." Zelenka suggested.

Zelenka flashed a smile, flirting with Esposito.

"Yes, yes. We all know what happened." Rodney chimed in, not wanting to be reminded that his actions lead to the deaths of a large number of living Ancients. His expression softens as he nods to Esposito again.

The door then opens.

"Ah! Voila." McKay gloated, then lead the way into the darkened room.

"You're just angry that you couldn't figure out how to override the Ancient protocols that kept us from shutting this place down remotely from the control room." Zelenka suspected

"Hey, neither could you." McKay shot back.

"Yes, but I didn't bet everyone a month's pay that I could do it." Was Radek's witty retort.

Rodney pointed a sharp finger at Zelenka.

"You." he paused, remembering the other people in the room.

"Okay, you know what? Look around, see if you can figure out how to turn this place offàwhatever it is." McKay said then approached a lighted panel on a one step podium and starts to hook up his tablet PC.

"Wait, are-are you sure you should be going up there?" Zelenka nervously objected.

"How else am I going to find out what this place does, huh?" McKay asked, then started muttering about there not being anything about the lab in the Ancient database, not bothering to keep his voice down.

"Oh, there probably is, we just don't have the time to. . ." Zelenka began, but stopped when Rodney managed to power up the device.

"Oh, here we go." Rodney announced.

"Ah. Okay, there should be a main power switch..." Radek explained trying to point to something on the control panel, but McKay impatiently brushes him off.

"Yes, I know that! What do you think I'm doing?" McKay harshly retorted.

"All right." Radek conceded.

Zelenka raises his arm back and runs it down his head, stepping further back. He fidgets, then gives a scheming grin. Almost as though he knows something that Rodney doesn't.

"All right, double or nothing."

Rodney scoffs. "Oh, you're on."

"All right." Zelenka said excitedly.

"All right. It's gonna be around here somewhere." Rodney said as he studied the panel.

Suddenly a panel overhead lights up, shining down on McKay. He looks up as a startled Zelenka and others step back.

While they watch a thin beam of light comes down from the overhead panel and entwines itself around McKay.

The system overloads and short circuits, sending electrical arcs around the room. Causing everyone to retreat ot a safe distance.

Finally the machine shuts down, leaving the room in darkness again.

Zelenka cautiously approaches.

"Rodney? What happened?" Zelenka wondered.

McKay turned to face Zelenka, his eyes wide with fear, and uncertainty.

"I'm not sure, but I think I just lost. Big time."

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Regardless of how things are looking, this will NOT be like the SGA episode it was based on.


	2. Ch 2 The Dark Path

Thanks for the reviews, I don't bite if they're constructive. Please read, review. Thanks.

Stargate Atlantis - The Dark Side of McKay

**Chapter 2 - The Dark Path**

McKay sat, waiting on an infirmary bed. Sheppard and Weir stood nearby as Beckett approached with a concerned look on his face.

"I did find an increased activity in his limbic system. But as far as I can tell, he's fine." Dr. Beckett explained. "But it doesn't appear to have any lasting effect."

"I was hit by a mysterious energy pulse. How can that possibly be fine?!"

"I've run every test I can. Blood work, M.R.I.s, X-rays, the lot. Other then the increased activity. I found no other anomalies in any of the results."Beckett reiterated.

"Okay, one more time—mysterious energy pulse! From a device created by the Ancients?! I mean, who knows what kind of long-term effects I could be in for." McKay started.

"I mean, there's gross mutation, giantism, invisibility…?" Rodney suggested.

Sheppard was paying limited attention, and replied simply. "That would be cool. I turned into a bug."

McKay stares at Sheppard, unable to believe his friends' calm, unconcerned reactions.

"All right, like I said, as far as I can tell, he's as healthy as a horse. I'm clearing you for active duty. But I want to get another MRI, and re-run your blood work every twelve hours."

McKay couldn't believe how callous, and unphased everyone was being.

"Are you insane?! Look, I need to be put under guard. Who knows what I could become!"

Elizabeth looked at Beckett. "What are the chances it could make him more pleasant?"

Elizabeth only batted an eye at Rodney. But looked at

Rodney at the end of her question.

"Oh, thank you." Rodney sarcastically responded.

"I'll keep an eye on him." Sheppard volunteered.

"Thank you." Elizabeth said then left

McKay's apprehension turned to blatant worry. "Can you still see me?"

**Ancient Lab **

Zelenka and McKay are working to get the lab operational. Sheppard sat nearby, reading a magazine. Everything is powered down.

Rodney let out an exasperated sigh.

"What are you saying?" Rodney demanded.

"Oh, that you were showing off." Zelenka chuckled. "Normally if Doctor Esposito weren't around, I doubt you would've been as reckless as you were.

"Are you insane?!" McKay shouted, almost infuriated by the insinuation.

"Which one's Esposito?" Sheppard wondered aloud, as though names weren't important.

"Oh, the-uh, the long dark hair?" Zelenka replied.

"Oh, right." Sheppard remembered. "The one with the perfect little—"

McKay was annoyed, as usual, and he cut off Sheppard "Do you mind? We're trying to work here."

"For the record, I was going to say "smile." Sheppard said, his tone betrayed nothing to convince Rodney.

"Yeah, sure you were, Kirk!" Rodney dubiously replied, then turned to Zelenka.

"What have you got?"

"Nothing. Whatever you did fried all the power conduits leading into the room." Zelenka replied

"Whatever I did?! Look, up until very recently, this lab was entirely underwater, quite possibly for over ten thousand years. How is that my fault?

"Well, that part of it isn't." Zelenka grudgingly agreed.

"Okay, that's it. I'm going for lunch." Rodney snapped, he was tired of hearing the discussion, and needed a break.

**Atlantis - Mess Hall**

McKay sat alone at a table, eating a sandwich and a variety of fruit. After a few moment he could hear his team's voices behind him.

"How is he doing?" Teyla asked.

"Same ol' Rodney." Sheppard replied.

"Are you sure? He looks a couple pounds heavier to me." Ronon teased.

"Ronon." Teyla scolded

"What? He eats all the time. It's not like he exercises." Ronon innocently defended.

McKay stopped chewing and looks down at his tray self-consciously.

"He's just feeding his unhappiness." Sheppard explained.

"Hello, I'm right here. I can—" McKay turned around to see the rest of his team sitting at a table at the far side of the crowded room. They were too far away to hear his response, but glance over when they see him looking at them.]

"I can hear you. Huh." McKay finished as he realized what was happening.

Geting up to join the others, he blindly reaches back for his tablet computer as he moves, and doesn't see it slide across the table telekinetically into his hand.

As McKay approached his comrades he began chastising them.

"For your information, I am exactly the same weight I've been since I got here. I need to eat regularly, otherwise I become hypoglycemic. And I am generally a very happy person."

McKay's rant was cut short by a technician over the intercom.

"Colonel Sheppard, please have your team report to the control room immediately. Colonel Sheppard."

The team stow their remaining comments and head for the control room.

**Atlantis - Control Room **

Joining the team in the control room, Weir begins.

"We received this transmission six minutes ago from Major Lorne's team."

"Atlantis base, repeat, we are under attack and cut off from the gate. I counted at least twenty, maybe more. Request backup immediately."

The message ended, Sheppard looked up, relative to the terminal.

"Where are they?" Sheppard asked.

"M72-656." Weir reported.

Sheppard wasted no time.

"Have a team of marines meet us in the jumper bay."

Atlantis Gate room - several minutes later.

A jumper lowers into the Gate Room. From the balcony, Weir watches it leave.

**Ancient Lab**

Zelenka continued his work on the panel as Weir entered.

"Doctor Weir? Any word?" Zelenka asked, concerned.

"Not yet. It has only been an hour. You wanted to see me." Weir Replied.

"Yes. I could use your help. Um, er, I managed to get power to part of the console to access the lab's research logs." Zelenka replied.

"Well, that's good news." Weir commented, with a minor sigh of relief.

"Well, I'm not so sure. Uh, I could use a second opinion." Zelenka said directing Weir to a display showing a lot of Ancient writing. Weir moved next to Zelenka at the console to take a closer look.

"It seems much of this refers to different elements of…human physiology."

Weir commented reading the display.

"It mentions the mutation of base genetic coding." Weir added

"I realize that Doctor Beckett said that there were no "evident" effects from Rodney's exposure to the device, but…it seems—" Zelenka started.

"It's meant to manipulate human DNA." Weir determined, and Zelenka finished.

It might also effect higher brain function, as a result." Zelenka warned.

The read was interrupted by a call over the intercom.

"Doctor Weir to the jumper bay. The rescue team has returned."

"Let's go." Weir directed.

**Atlantis - Jumper bay**

Weir and Zelenka arrive just as Sheppard's jumper door opens.

"What could I have done?" Rodney asked.

"You could have acted faster." Sheppard said defeated.

"What are you talking about?" McKay snapped.

"That thing you did, just before everyone else ran away." Sheppard snapped.

"Colonel?" Weir asked

"We lost two of Lorne's men."

As you may have noticed, this is where things stray down . . . "The Dark Path". Thank you for reading please leave a review on your way out to other good reads.


	3. Ch 3 Fallen Heroes

Now if you thought Chapter 2 was dark, you haven't seen anything yet. Well, you'll just have to read. Enjoy.

**Stargate Atlantis - The Dark Side of McKay**

**Chapter 3 - Fallen Heroes**

Beckett and a medical team arrive with gurneys.

"How bad is it, and who's been hit?" Beckett asked, knowing the someone has been injured.

"I lost two of my guys, Doc. But the rest of us are alive, thanks to…McKay."

"So he says." Sheppard said upset, but who wouldn't be?

Dr. Weir wasn't getting the answers she wanted, or needed for that matter.

"Rodney?"

"Well, to be honest, I'm not entirely sure. I wasn't even sure it was me, at first. But, uh, the correlation's impossible to ignore. I saw Lorne's team pinned down, the bad guys closing in, I just thought, uh, wouldn't it be great if all of their weapons jammed…at the same time." McKay explained.

Teyla studied McKay closely, shaking her head. Sheppard looks amused and openly doubtful.

"Look, next thing I know, they're all running away, so…"

"So you think because you wanted it to happen, it just did."

It was a little more than that.

Weir looked skeptical as well. McKay fidgeted, frustrated.

"Okay, you know what? Watch this! I'll uh…" McKay said looking around, finally pointing at Beckett, who is lifted off the floor and hung suspended in mid-air. Everyone watched in shock.

"Uh, Rodney!"

Weir approached worried.

"Rodney…?"

"Believe me, I find this as disturbing as you do." Rodney replied.

"Like bloody hell you do!" Came Carson's retort

"Put him down." weir calmly pleaded.

"Right."

McKay lowered his hand, and Beckett slowly drifted to the floor, sighing in relief.

"It's a shame you didn't think of this BEFORE my men were killed." Lorne snapped.

"Major!" Weir said sternly.

"He could have saved them, he let them die." Lorne said, then stormed out.

**Atlantis - Infirmary**

McKay lies in an infirmary bed. Sheppard and Weir stand at his bedside.

"Have there been any other instances of this…power manifesting itself?" Weir asked.

"Powers. Plural.." McKay snapped.

Weir paused, McKay was becoming something his colleagues have never seen.

"What else can you do besides telekinesis?" Weir asked.

"Well, super-hearing for one, and I'm not sure, but I may actually be getting smarter. It's hard to say for sure, because I was-I was pretty smart to start with, but, um, recently I've been having some ideas that I don't think even I would've thought of before." Rodney said quickly amid a few insults.

"Does superego count as a power?" Sheppard interjected.

McKay spotted a staff member bringing him a tray of food.

"Oh, finally! Look, keep it coming." McKay said.

McKay took the tray and began to cut into the food.

"He could also be dealing with a "super" appetite. Although, it's hard to tell, because he ate so much before."

"You want to knock it off?" Rodney chided

"You're kidding me, he's eating again?" Beckett asked

"I have a very active metabolism. Do you want to see me become hypoglycemic?" Rodney ranted.

"Aye, among other problems. The scans show a dramatic increase in synaptic interaction throughout all the sections of Rodney's brain, much higher than normal human levels.

McKay paused in his eating, looking momentarily concerned. He took his next bite more slowly.

"There was an incident at SGC just over a year ago. Weir began. "SG-1 discovered a highly evolved human being in stasis. Turned out, he was the result of experimentation by a Goa'uld named Anubis. He was trying to create a means of artificially accelerating the human physiology to the point of ascension.

"Well, gee. Maybe that device I found must have been some kind of an accelerator. We know that the Ancients developed all kinds of powers as they evolved. It was just a matter of bad luck that we didn't run into that lab earlier. Seriously, me a superhero. Who would've thought it?"

Obviously irate, he eats his meal with furious vigor.

**Atlantis - Lab**

A team worked on studying the device. Among them are Weir, translating the logs, and Sheppard, who stood nearby.

"Look, we all agree the Ancients were pretty screwed up." Sheppard said.

"We do?" Weir asked, she wasn't paying full attention.

"All the ones I met were arrogant and condescending, and not for good reason. They made giant mistakes and never fixed them."

"They were still human." Weir defended.

"Then there were all those crazy rules." Sheppard griped.

"Those only came after they ascended." Weir clarified.

"Whatever. I—maybe this thing doesn't work on everyone, who knows? But we do know it works on McKay." Sheppard began.

"It has only been a day." weir admonished.

"Assuming it's safe. Well, to be honest, even if it's not. If we can get a significant advantage over the Wraith and Replicators—" Sheppard began.

"John, I agree. This device may have great potential…" Weir warned.

"And with great potential comes great responsibility. I know." Sheppard was near to getting to his point.

"Like a lot of other things we have found in this city, it is a very advanced piece of technology. For all we know, it could also be very dangerous." Weir warned.

"I'm just saying…" Sheppard said arriving at his point.

"Yes, you can be next." Weir promised.

"Thank you." Sheppard said, smiling.

"John, can I ask you something? Have you noticed a change in Rodney?" Weir asked.

"You mean besides the super powers?" Sheppard asked.

"He's. . ." Weir began.

"Ruder than he was two days ago?" Sheppard confirmed.

Sheppard left. Zelenka approaches. He had overheard the conversation.

"You know, if you're compiling a list…I-I'd…"

"Could we stay focused, please?" Weir begged.

**Atlantis - Infirmary**

McKay waited in the infirmary. Guards waited at the entrance.]

"Come on, you can't keep me cooped up in here forever." McKay seemed angry, but kept his voice down.

"You might not be sick, Rodney, but I think we can both agree what's happening here is far from normal. And have you not noticed you seem quite . . . irritated." Beckett explained.

"Exactly, so let go out of here." McKay spat.

"I'm serious! We have no idea of the extent of your genetic mutation."

"Please, it's not mutation. It's an advancement." McKay corrected.

"Until we know exactly what's going on here…" Beckett began to explain.

"Carson, I'm still me. Anyway, it's not like you or, these guys could stop me from leaving any ways." McKay said gesturing to the guards at the door, who look on warily.

"No, but I could." Ronon said entering the Infirmary.

"Oh, you care to put that to a test?"

Ronon stepped up to Rodney, bringing his face to within a few inches.

"Do you?"

"Well…no. Not really." McKay backed down.

"Any ways, as I was saying, I think you're fine to go about your daily duties, as long as you have someone with you. And you—" Becket was cut off by McKay.

"Check in every couple of hours. Yes, yes. Ba-bye!"

McKay stormed out with Ronon warily as his heels.

"Thanks for getting me out of there, but I'm going to my quarters and taking a nap." McKay said then started to walk away. But Ronon grabbed McKay's arm, and was thrown back by a wave of telekinetic energy.

McKay looked shocked, and terrified

"I'm sorry. I-I . . . just reacted." Rodney said, then helped Ronon onto his feet.

McKay and Ronon continued down the crowded corridor.

"I don't know what happened." Rodney began stuttering.

"Forget it." Ronon said, there was genuine concern in his voice.

Passing Esposito, McKay stops short, then looked at Esposito.

"Really?" Rodney asked.

"What?" Esposito asked.

"I did not need to hear that.

"Great." McKay said sarcastically.

"What?" Ronon asked.

"She thinks I'm hot." Rodney said, pointing at Esposito.

"I-I didn't say anything." Esposito said, embarassed.

"Oh, no-no-no. I'm sure that you…uh… Oh, of course, no, I should've known." Rodney said then turned to Ronon. "She meant you."

"I don't know what you're talking about." Esposito said then hurried away.

"McKay, she didn't say a word." Ronon said, he also wanted to hurry away.

"Oh great. I can read minds. Oh, this is going to get old -- Real fast!" Rodney said, then walked away towards Weir's office

**Atlantis - Weir's office.**

Weir was working when McKay entered, Ronon following. Weir looked around, about to speak.

"Oh, I'm fine…No…No…And...no." Rodney said.

"What?" Weir asked, confused.

"I can read your mind. Uh, everyone's actually. I'm finding it a little disturbing, so I'm trying to tune it out as much as I possibly can." Rodney explained. "Well, um, sort of. Anyways, Look, I, uh, wanted to get your permission to access the control chair. I've, uh, got some, um, pretty interesting ideas for maximizing our ZPM by, uh, reconfiguring the city's power systems. It's too complicated to explain, but, uh, trust me when I say that you are going to be incredibly happy with the results.

Before Weir could speak.

"Look, Elizabeth, I-I know you have every right not to trust me, but, I'm going to make things much-much better. Okay?

McKay paused for the merest second.

"Fine."

Rodney turns to leave.

"I'm going back to my quarters so I don't take over the city for my own evil purposes." McKay said then turned and left.

McKay was almost to the chair room when Ronon realized where he was going.

"This is the way to the chair room." Ronon said.

"I know!" Rodney said, then Ronon heard a beep coming from his gun, looking down he accidentally gave Rodney the time he needed to turn and throw Ronon down the corridor.

Hitting the ground Ronon slid, and crashed through a window overlooking the ocean.

Is Ronon dead? Who else gets in Rodney's way? What other dark things befall Atlantis?


	4. Ch 4 The Beginning of the End

As you might have noticed, the last 3 chapters followed the episode quite closely. But all good things must come to an end. This is where Rodney begins to show his Dark side, and the Rodney we all know and love, goes away.

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**Stargate Atlantis - The Dark Side of McKay**

**Chapter 4 - The Beginning of the end.**

Arriving at the Chair control room, McKay did a brief visual survey to see the room was clear, then sealed the door.

Without hesitation, McKay heads for the chair, sits down, and the chair reclines, after a split second, a hologram of the city appears over McKay.

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**Atlantis - Control Room**

Sheppard arrives and proceeded up the stairs and into Weirs office, where she was researching Ancient History.

"Have you seen McKay? I can't raise him on the radio." Sheppard asked.

"He was here a few minutes ago, he asked to use the chair. When I said "No", he said he was going to his quarters." Weir replied.

"Did anyone else see him?" Sheppard asked.

"I would imagine so. Ronon was with him." Weir elaborated.

Sheppard activated the link on his headset.

"Ronon, this is Sheppard."

When there was no response he tried again.

"Ronon, this is Sheppard, come in."

When Ronon did not respond, Sheppard began looking concerned.

"I think we have a problem." Sheppard said.

Sheppard and Weir made a bee-line for McKay's quarters.

"Why am I reminded more and more of that incident at Stargate Command?" Weir asked.

Soon Sheppard and Weir arrived at McKay's quarters.

Sheppard hit the chime.

No response. Sheppard hit it again.

Again, no response.

Weir activated the link on her headset.

"Chuck, this is Weir. We need into McKay's quarters." Weir said, and after a second the door to McKay's quarters opened.

Walking in, Sheppard noticed McKay wasn't in his bed, Sheppard made his usual comment.

"He's not in his bed." Sheppard noted.

"Which begs the question: Where is he?" Weir asked.

Then a disturbing call came in.

"Dr. Weir. Someone has sealed them selves in the chair room, and they're not responding."

"We're on our way." Weir replied, while Sheppard called for a team of Marines.

"I've got a bad feeling about this." Sheppard commented, then lead the way out into the corridor.

Arriving at the Chair room Weir was briefed on the situation.

"Who ever is in there, they've managed to stay ahead of us. Blocking any way of gaining entry into the room."

"What about C-4?" Sheppard asked.

"Are you sure someone is in there?" Weir asked not wanting to resort to blowing something up..

"Positive."

Weir was handed a life-signs-detector and it showed a blip in the Chair Control room.

It was clear that McKay was in the Chair room.

Then all power was cut from the entire city.

Sheppard turned to the nearest Marine.

"We need some C-4, now!"

Sheppard stopped when he heard a voice on the intercom.

"I'm afraid I can't allow you in here."

"McKay?" Sheppard asked.

"Who else would it be?" McKay asked in a dark tone, almost sinister and mono-toned.

"Open the door, McKay!" Sheppard demanded impatiently.

"I can't do that." McKay replied.

With those words something begins spewing out of a nearby pipe.

"Fire Suppressant, get out of here." Weir shouted.

"You heard her, everyone out!" Sheppard mirrored.

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Thank you, reviews are welcome, whether constructive or ego massaging. Please bear in mind I think I had to make up a few things.


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